Structure Optimization (Gaussian)

This page covers geometry optimization workflows using Gaussian.

Geometry Optimization

Run basic geometry optimization to find the minimum energy structure:

chemsmart sub [OPTIONS] gaussian [GAUSSIAN_OPTIONS] opt [SUBCMD_OPTIONS]

Optimization Options

Option	Type	Description
`-f, --freeze-atoms`	string	Atom indices to freeze (1-based indexing)

Basic Usage

Standard geometry optimization:

chemsmart sub gaussian -p project -f input.gjf -c 0 -m 1 opt

Constrained optimization with frozen atoms:

# Freeze atoms 1-10
chemsmart sub gaussian -p project -f input.com opt -f 1-10

# Freeze atoms 1, 2, 3, 5, and 7
chemsmart sub gaussian -p project -f input.com opt -f 1-3,5,7

Solvated Optimization

Solvent options are specified at the Gaussian group level (before the opt subcommand) and apply to all job types. See Solvent Options for the full option reference.

Gas phase optimization (project default, no solvent):

chemsmart sub gaussian -p anomer -f molecule.xyz -c 0 -m 1 -a no_solv opt

Add SMD solvation for a single run without modifying the project settings:

chemsmart sub gaussian -p anomer -f molecule.xyz -c 0 -m 1 -sm smd -si water -a solv opt

With an additional SCRF option (e.g. iterative solver):

chemsmart sub gaussian -p anomer -f molecule.xyz -c 0 -m 1 -sm smd -si water -so iterative -a solv opt

Remove solvent when the project settings already specify one:

chemsmart sub gaussian -p solv_project -f molecule.xyz -c 0 -m 1 --remove-solvent -a gas opt

Examples

Optimization from a previous output file:

Use an optimized structure with different charge/multiplicity:

chemsmart sub -s SLURM gaussian -p project -f k_atom_opt.log -c 1 -m 1 -l k_cation_opt opt

This takes the optimized K atom structure and runs a cation optimization.